DFT Calculations on the Effect of Solvation on the Tautomeric Reactions for Wobble Gua-Thy and Canonical Gua-Cyt Base-Pairs

Kazuya Nomura, Ryota Hoshino, Eisuke Shimizu, Yasuhiro Hoshiba, Victor I. Danilov, Noriyuki Kurita

Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Japan.
Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine.

DOI: 10.4236/jmp.2013.43A059                

Abstract

To elucidate the reaction mechanism from wobble Guanine-Thymine (wG-T) to tautomeric G-T base-pairs, we investigate its transition state (TS) by density functional theory (DFT) calculations, in vacuum and in water approximated by continuum solvation model. From the comparison of these results, we attempt to elucidate the effect of solvation on the tautomeric reaction for wG-T. In addition, the same DFT calculations are performed for the canonical G-C base-pair, in order to reveal the difference in the activation energy for the reactions involving wG-T and G-C. The obtained TS structures between wG-T and G*-T/G-T* (asterisk is an enol-form of base) are almost the same in vacuum and in water. However, the activation energy is 16.6 and 19.1 kcal/mol in vacuum and in water, respectively, indicating that the effect of solvation enlarges the energy barrier for the reactions from wG-T to G-T*/G*-T. The activation energy for the tautomeric reaction from G-C to G*-C* is also evaluated to be 15.8 and 12.9 kcal/mol in vacuum and in water, respectively. Therefore, it is expected that the tautomeric reaction from wG-T to G*-T/G-T* can occur in vacuum with a similar probability as that from G-C to G*-C*. We furthermore investigate the TS structure for wG-BrU to reveal the effect of the BrU introduction into wG-T. The activation energy is 14.5 and 16.7 kcal/mol in vacuum and in water, respectively. Accordingly, the BrU introduction is found to increase the probability of the tautomeric reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G bases is accelerated by the introduction of wG-BrU base-pair.

Keywords

DFT; Wobble Base Pair; Base Pair; Tautomerization; Transition State; Activation Energy; Solvation

Conflicts of Interest

The authors declare no conflicts of interest.

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